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NextSeq System
Site Prep Guide
For Research Use Only. Not for use in diagnostic procedures.
Revision History
Introduction
Delivery and Installation
Laboratory Requirements
Electrical Requirements
Uninterruptible Power Supply
Environmental Considerations
Network Considerations
Antivirus Software
User-Supplied Consumables and Equipment
Technical Assistance
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ILLUMINA PROPRIETARY
Document # 15045113 v01
October 2015
This document and its contents are proprietary to Illumina, Inc. and its affiliates ("Illumina"), and are intended solely for the contractual use of its customer in connection with the use of the product(s) described herein and for no other purpose. This document and its contents shall not be used or distributed for any other purpose and/or otherwise communicated, disclosed, or reproduced in any way whatsoever without the prior written consent of Illumina. Illumina does not convey any license under its patent, trademark, copyright, or common-law rights nor similar rights of any third parties by this document.
The instructions in this document must be strictly and explicitly followed by qualified and properly trained personnel in order to ensure the proper and safe use of the product(s) described herein. All of the contents of this document must be fully read and understood prior to using such product(s).
FAILURE TO COMPLETELY READ AND EXPLICITLY FOLLOW ALL OF THE INSTRUCTIONS CONTAINED HEREIN
MAY RESULT IN DAMAGE TO THE PRODUCT(S), INJURY TO PERSONS, INCLUDING TO USERS OR OTHERS, AND
DAMAGE TO OTHER PROPERTY.
ILLUMINA DOES NOT ASSUME ANY LIABILITY ARISING OUT OF THE IMPROPER USE OF THE PRODUCT(S)
DESCRIBED HEREIN (INCLUDING PARTS THEREOF OR SOFTWARE).
© 2015 Illumina, Inc. All rights reserved.
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Epicentre, ForenSeq, Genetic Energy, GenomeStudio, GoldenGate, HiScan, HiSeq, HiSeq X, Infinium, iScan, iSelect,
MiSeq, MiSeqDx, MiSeq FGx, NeoPrep, NextBio, Nextera, NextSeq, Powered by Illumina, SureMDA, TruGenome,
TruSeq, TruSight, Understand Your Genome, UYG, VeraCode, verifi, VeriSeq, the pumpkin orange color, and the streaming bases design are trademarks of Illumina, Inc. and/or its affiliate(s) in the U.S. and/or other countries. All other names, logos, and other trademarks are the property of their respective owners.
Revision History
Document
Document # 15045113 v01
15045113 G
15045113 F
15045113 E
15045113 D
15045113 C
15045113 B
15045113 A
Date
October
2015
May
2015
March
2015
February
2015
August
2014
May
2014
February
2014
January
2014
Description of Change
Specified that an equivalent to the recommended supplier of
NaOCl is a laboratory-grade equivalent.
Corrected table heading from power consumption to power supply rating.
Removed Live Help from the list of purposes for an internet connection. This feature was removed from the control software.
Updated list of Additional Resources to remove the kit reference guides. See the NextSeq 500 System Guide (document # 15046563) or NextSeq 550 System Guide (document # 15069765) for preparation instructions and see the NextSeq Kit support page on the Illumina website for information about kit contents and compatibility.
Updated user-supplied consumables to specify consumables required for sequencing and consumables required for instrument maintenance.
Changed the title of the guide to specify the NextSeq system. This guide applies to the NextSeq 500 and the NextSeq 550.
Updated user-supplied consumables to specify uses of NaOCl for manual wash options introduced in NCS v1.4.
Updated network considerations to specify that a 10 Mbps network connection is recommended for using BaseSpace.
Corrected network cable size from CAT6 to CAT 5E.
Added antivirus software recommendation.
Added compatibility recommendations for network maintenance activities.
Updated VWR catalog # for alcohol wipes to 95041-714.
Updated SDS link to support.illumina.com/sds.html.
Added NextSeq Custom Primers Guide (document # 15057456) to
Additional Resources.
Updated network connections to emphasize that the instrument is designed for use with a network, even when running in standalone mode. Specified a minimum connection of 10 Mbps.
Updated user-supplied consumables list to specify 3%–6% sodium hypochlorite and list a supplier catalog number.
Initial release.
NextSeq System Site Prep Guide
3
Introduction
This guide provides specifications and guidelines for preparing your site for installation and operation of the Illumina ® NextSeq ® 500 and NextSeq ® 550 systems:
}
Laboratory space requirements
}
Electrical requirements
} Environmental constraints
}
Computing requirements
}
User-supplied consumables and equipment
Safety Considerations
See the NextSeq System Safety and Compliance Guide (document # 15046564) for important information about safety considerations.
Additional Resources
The following documentation is available for download from the Illumina website.
Resource
NextSeq System Safety and
Compliance Guide (document #
15046564)
RFID Reader - Model # TR-001-
44 User Guide (document #
15041950)
Denaturing and Diluting Libraries for the NextSeq System (document
# 15048776)
NextSeq Custom Primers Guide
(document # 15057456)
NextSeq 500 System Guide
(document # 15046563) or
NextSeq 550 System Guide
(document # 15069765)
BaseSpace help
(help.basespace.illumina.com)
Description
Provides information about operational safety considerations, compliance statements, and instrument labeling.
Provides information about the RFID reader in the instrument, compliance certifications, and safety considerations.
Provides instructions for denaturing and diluting prepared libraries for a sequencing run, and preparing an optional
PhiX control. This step applies to most library types.
Provides information about using custom sequencing primers in place of Illumina sequencing primers.
Provides an overview of instrument components, instructions for operating the instrument, and maintenance and troubleshooting procedures.
Provides information about using BaseSpace
® and available analysis options.
Visit the NextSeq support pages on the Illumina website for access to documentation, software downloads, online training, and frequently asked questions.
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Document # 15045113 v01
Delivery and Installation
An authorized service provider delivers the system, uncrates components, and places the instrument on the lab bench. Make sure that the lab space and bench are ready before delivery.
CAUTION
Only authorized personnel can uncrate, install, or move the instrument. Mishandling of the instrument can affect the alignment or damage instrument components.
An Illumina representative installs and prepares the instrument. When connecting the instrument to a data management system or remote network location, make sure that the path for data storage is selected before the date of installation. The Illumina representative can test the data transfer process during installation.
CAUTION
After your Illumina representative has installed and prepared the instrument, do not relocate the instrument. Moving the instrument improperly can affect the optical alignment and compromise data integrity. If you have to relocate the instrument, contact your Illumina representative.
Crated Dimensions and Contents
The NextSeq system is shipped in one crate. Use the following dimensions to determine the minimum door width required to accommodate the shipping container.
Measurement Crated Dimensions
Height
97 cm (38 in)
Width
90 cm (35.5 in)
Depth
90 cm (35.5 in)
Weight
151.5 kg (334 lb)
The crate contains the instrument along with the following components:
}
Spent reagents bottle
}
Reagent wash cartridge and buffer wash cartridge
} BeadChip adapter
}
Power cord
}
NextSeq 500 System Guide (document # 15046563) or NextSeq 550 System Guide
(document # 15069765)
}
NextSeq System Safety and Compliance Guide (document # 15046564)
}
RFID Reader - Model # TR-001-44 User Guide (document # 15041950)
}
Accessories kit, which contains the following components:
}
Keyboard and mouse
} Network cable, shielded CAT 5e
NextSeq System Site Prep Guide
5
Laboratory Requirements
This section provides specifications and requirements for setting up your lab space. For more information, see
Environmental Considerations on page 10 .
Instrument Dimensions
Measurement Instrument Dimensions (Installed)
Height
58.5 cm (23 in)
Width
53.4 cm (21 in)
Depth
63.5 cm (25 in)
Weight
83 kg (183 lb)
Placement Requirements
Position the instrument to allow proper ventilation, access to the power switch and power outlet, and access for servicing the instrument.
}
Make sure that you can reach around the left-side of the instrument to access the power switch on the back panel.
} Position the instrument so that personnel can quickly disconnect the power cord from the outlet.
}
Make sure that the instrument is accessible from all sides.
Access Minimum Clearance
Sides
Allow at least 61 cm (24 in) on each side of the instrument.
Rear
Allow at least 10.2 cm (4 in) behind the instrument.
Top
Allow at least 61 cm (24 in) above the instrument.
CAUTION
Moving the instrument improperly can affect the optical alignment and compromise data integrity. If you have to relocate the instrument, contact your Illumina representative.
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Lab Bench Guidelines
The instrument includes precision optical elements. Place the instrument on a sturdy lab bench away from sources of vibration.
Width
122 cm (48 in)
Height
91.4 cm (36 in)
Depth
76.2 cm (30 in)
Casters
Optional
Vibration Guidelines
Use the following guidelines to minimize vibrations during sequencing runs and ensure optimal performance:
}
Place the instrument on a sturdy lab bench.
} Do not place other equipment on the bench that can produce vibrations, such as a shaker, vortexer, centrifuge, or instruments with heavy fans.
}
Do not place objects on top of the instrument.
}
When the instrument is sequencing, do not open the reagent compartment door, buffer compartment door, right service panel, or flow cell door.
Lab Setup for PCR Procedures
Some library prep methods require the polymerase chain reaction (PCR) process.
Establish dedicated areas and lab procedures to prevent PCR product contamination before you begin work in the lab. PCR products can contaminate reagents, instruments, and samples, causing inaccurate results and delay normal operations.
Establish Pre-PCR and Post-PCR Areas
} Establish a pre-PCR area for pre-PCR processes.
}
Establish a post-PCR area for processing PCR products.
}
Do not use the same sink to wash pre-PCR and post-PCR materials.
} Do not use the same water purification system for pre-PCR and post-PCR areas.
} Store supplies used in pre-PCR protocols in the pre-PCR area, and transfer to the post-PCR area as needed.
Dedicate Equipment and Supplies
}
Do not share equipment and supplies between pre-PCR and post-PCR processes.
Dedicate a separate set of equipment and supplies in each area.
} Establish dedicated storage areas for consumables used in each area.
Required Storage for Sequencing Consumables
Item ( 1per run)
Reagent cartridge
Buffer cartridge
Flow cell cartridge
Storage Requirement
-25°C to -15°C
15°C to 30°C
2°C to 8°C
NextSeq System Site Prep Guide
7
Electrical Requirements
Power Specifications
Type
Line Voltage
Power Supply Rating
Specification
100–240 Volts AC @ 50/60 Hz
600 Watts, maximum
Receptacles
Your facility must be wired with the following equipment:
}
For 100–120 Volts AC—A 15 Amp grounded, dedicated line with proper voltage and electrical ground is required. North America and Japan—Receptacle: NEMA 5-15
}
For 220–240 Volts AC—A 10 Amp grounded line with proper voltage and electrical ground is required. If the voltage fluctuates more than 10%, a power line regulator is required.
Protective Earth
The instrument has a connection to protective earth through the enclosure.
The safety ground on the power cord returns protective earth to a safe reference. The protective earth connection on the power cord must be in good working condition when using this device.
Power Cords
The instrument comes with an international standard IEC 60320 C20 receptacle and is shipped with a region-specific power cord.
Hazardous voltages are removed from the instrument only when the power cord is disconnected from the AC power source.
To obtain equivalent receptacles or power cords that comply with local standards, consult a third-party supplier such as Interpower Corporation (www.interpower.com).
CAUTION
Never use an extension cord to connect the instrument to a power supply.
Fuses
The instrument contains no user-replaceable fuses.
Only Illumina Field Service Engineers are qualified to replace the internal fuses. The power entry module includes 2 input fuses on the high-voltage input lines. These fuses are rated for 7 Amps, 250 VAC, Slo-Blo.
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Document # 15045113 v01
Uninterruptible Power Supply
A user-supplied uninterruptible power supply (UPS) is highly recommended. Illumina is not responsible for runs affected by interrupted power regardless of whether the instrument is connected to a UPS. Standard generator-backed power is often not uninterruptible and a brief power outage is typical before power resumes.
The following table lists region-specific recommendations.
Specification
Input Frequency
APC Smart UPS
2200 VA LCD 120 V
(Japan/North America)
Maximum Power
1920 W
Input Voltage
(nominal)
100–120 VAC
50/60 Hz
Input Connection
NEMA 5-20P
Typical Run Time
(300 W)
90 minutes
Typical Run Time
(600 W)
40 minutes
APC Smart UPS
2200 VA LCD 230 V
(International)
1980 W
220–240 VAC
50/60 Hz
IEC-320 C20
90 minutes
40 minutes
To obtain an equivalent UPS that complies with local standards for facilities outside the referenced regions, consult a third-party supplier such as Interpower Corporation
(www.interpower.com).
NextSeq System Site Prep Guide
9
Environmental Considerations
Element
Temperature
Humidity
Elevation
Air Quality
Ventilation
Specification
Maintain a lab temperature of 19°C to 25°C (22°C ±3°C). This temperature is the operating temperature of the instrument.
During a run, do not allow the ambient temperature to vary more than ±2°C.
Maintain a noncondensing relative humidity between 20–80%.
Locate the instrument at an altitude below 2000 meters (6500 feet).
Operate the instrument in a Pollution Degree II environment or better. A Pollution Degree II environment is defined as an environment that normally includes only nonconductive pollutants.
Consult your facilities department for ventilation requirements based on the instrument heat output specifications.
Heat Output
Measured Power
600 Watts
Thermal Output
2048 BTU/hour
Noise Output
Noise Output
(dB)
< 60 dB
Distance from Instrument
1 meter (3.3 feet)
A measurement of < 60 dB is within the level of a normal conversation at a distance of approximately 1 meter (3.3 feet).
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Document # 15045113 v01
Network Considerations
The NextSeq system is designed for use with a network, regardless of whether runs are connected to BaseSpace or performed in standalone mode.
Performing a run in standalone mode requires a network connection to transfer run data to a network location. Do not save run data to the local hard drive on the NextSeq system. The hard drive is intended for temporary storage before data are transferred automatically. Any data saved on the hard drive beyond the current run fills the hard drive and prevents subsequent runs until space is made available.
An internet connection is required for the following operations:
}
Connect to Illumina BaseSpace ® or BaseSpace ® Onsite.
} Install updates to the NextSeq Control Software (NCS) from the system interface.
Network Connections
Use the following recommendations to install and configure a network connection:
}
Use a 1 gigabit connection between the instrument and your data management system. This connection can be made directly or through a network switch.
} For network connections, a shielded CAT 5e network cable of 3 meters (9.8 feet) in length is provided with the instrument.
}
Configure Windows Updates to prevent automatic updates.
}
If you are using BaseSpace, use a minimum network connection of 10 Mbps.
Network Support
Illumina does not install or provide technical support for network connections.
Review network maintenance activities for potential compatibility risks with the
Illumina system, including the following risks:
}
Removal of the Group Policy Objects (GPOs)—GPOs can affect the operating system (OS) of connected Illumina resources. OS changes can disrupt the proprietary software in Illumina systems.
} Illumina instruments have been tested and verified to operate correctly. After connecting to domain GPOs, some settings might affect the instrument software. If the instrument software operates incorrectly, consult your facility IT administrator about possible GPO interference.
}
Activation of Windows Firewall and Windows Defender—These Windows products can affect the OS resources used by Illumina software. Install antivirus software to protect the instrument control computer.
}
Changes to the privileges of preconfigured users—Maintain existing privileges for preconfigured users. Make preconfigured users unavailable as needed.
}
Potential IP address conflicts—The NextSeq has fixed internal IP addresses, which can cause system failure in the case of conflicts.
NextSeq System Site Prep Guide
11
Antivirus Software
An antivirus software of your choice is highly recommended to protect the instrument control computer against viruses.
To avoid data loss or interruptions, configure the antivirus software as follows:
} Set for manual scans. Do not enable automatic scans.
}
Perform manual scans only when the instrument is not in use.
}
Set updates to download without user authorization, but not install.
} Do not update during instrument operation. Update only when the instrument is not running and when it is safe to reboot the instrument computer.
}
Do not reboot the computer automatically upon update.
}
Exclude the application directory and data drive from any real-time file system protection. Apply this setting to the C:\Illumina directory and the D:\ drive.
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Document # 15045113 v01
User-Supplied Consumables and Equipment
The following consumables and equipment are used on the NextSeq system. For more information, see the NextSeq 500 System Guide (document # 15046563) or NextSeq 550
System Guide (document # 15069765).
User-Supplied Consumables for Sequencing Runs
Consumable
1 N NaOH
(sodium hydroxide)
200 mM Tris-HCl, pH7
Alcohol wipes, 70% Isopropyl or
Ethanol, 70%
Disposable gloves, powderfree
Lab tissue, low-lint
Supplier
General lab supplier
General lab supplier
VWR, catalog # 95041-714
(or equivalent)
General lab supplier
General lab supplier
VWR, catalog # 21905-026
(or equivalent)
Purpose
Library denaturation, diluted to
0.2 N
Library denaturation
Flow cell cleaning and general purpose
General purpose
Flow cell cleaning
User-Supplied Consumables for Instrument Maintenance
Consumable
NaOCl, 5%
(sodium hypochlorite)
Tween 20
Water, laboratory-grade
Supplier Purpose
Sigma-Aldrich, catalog #
239305
(or laboratory-grade equivalent)
Washing the instrument using the manual post-run wash; diluted to 0.12%
Sigma-Aldrich, catalog # P7949 Washing the instrument using manual wash options; diluted to 0.05%
General lab supplier Washing the instrument
(manual wash)
Guidelines for Laboratory-Grade Water
Always use laboratory-grade water to perform instrument procedures. Never use tap water or deionized water. The following are examples of acceptable laboratory-grade water:
}
Illumina PW1
}
18 Megohm (MΩ) water
} Milli-Q water
} Super-Q water
}
Molecular biology-grade water
User-Supplied Equipment
Item
Freezer, -25°C to -15°C, frost-free
Ice bucket
Refrigerator, 2°C to 8°C
Source
General lab supplier
General lab supplier
General lab supplier
NextSeq System Site Prep Guide
13
Notes
Technical Assistance
For technical assistance, contact Illumina Technical Support.
Table 1 Illumina General Contact Information
Website
www.illumina.com
Table 2 Illumina Customer Support Telephone Numbers
Region
North America
Australia
Austria
Belgium
Denmark
Finland
France
Germany
Ireland
Contact Number
1.800.809.4566
1.800.775.688
0800.296575
0800.81102
80882346
0800.918363
0800.911850
0800.180.8994
1.800.812949
Region
Italy
Netherlands
New Zealand
Norway
Spain
Sweden
Switzerland
United Kingdom
Other countries
Contact Number
800.874909
0800.0223859
0800.451.650
800.16836
900.812168
020790181
0800.563118
0800.917.0041
+44.1799.534000
Safety data sheets (SDSs)—Available on the Illumina website at
support.illumina.com/sds.html
.
Product documentation—Available for download in PDF from the Illumina website. Go to support.illumina.com, select a product, then select Documentation & Literature.
NextSeq System Site Prep Guide
Illumina
San Diego, California 92122 U.S.A.
+1.800.809.ILMN (4566)
+1.858.202.4566 (outside North America) [email protected]
www.illumina.com
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